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Post ancient calculator results/comparisons with ancient dna here
I thought this thread could be an interesting/fun thing to do with ancient dna samples by how much you share with each sample(s).
All you have to to do is take your raw data that is a compressed zip file and hit the browse button for your autosomal file and it will calculate your percentage(s).
You can download and click on the hyperlink here: http://www.y-str.org/2014/12/ancient-calculator.html
Sample descriptions if you don't feel like going through all the clicking to look at each one individually (Can be found here: http://www.y-str.org/p/ancient-dna.html):
Ajvide 58: Sample Location: Sweden
Gedmatch Kit number: F999924
Gender: Male
Y-DNA: I-CTS772
Mt-DNA: U4d
Approximate Age: 5000 years
Description:The authors had generated between 0.01 to 2.2-fold genome wide coverage for 6 neolithic hunter-gathers from pitted ware culture, 4 neolithic farmers from funnel beaker culture and 1 late Mesolithic hunter-gatherer. I converted the raw data of Ajvide58 from Pitted Ware Culture excavated in Sweden into formats familiar to genetic genealogists. I also filtered with SNPs tested by DNA testing companies like FTDNA, 23andMe and Ancestry in order to upload to GEDMatch as kit# F999924.
Ajvide58 DNA Samples: http://www.fi.id.au/2014/10/ajvide58-dna-analysis.html
Altai Neanderthal: Sample Location: Denisova Cave, Siberia
Gedmatch kit number: F999902
Gender: Female
Approximate age: 50,000 years
Australian Aboriginal: Sample location: "Western Australian"
Gender: Male
Y-DNA: F-M235
Mt-DNA: O1a
Approximate Age: 100 years
Description:The authors presented an Aboriginal Australian genomic sequence obtained from a 100-year-old lock of hair donated by an Aboriginal man from southern Western Australia in the early 20th century. The nuclear genome was sequenced to an overall depth of 6.4-fold. It had a high degree of fragmentation, but no genotype level evidence of sample contamination by DNA from sample handlers of European descent was detected. I converted this genome into formats familiar to genetic genealogists. I also filtered with SNPs tested by DNA testing companies like FTDNA, 23andMe and Ancestry in order to upload to GEDMatch but found this ancient DNA has less SNPs that are common with them. Hence, I did not upload this to GEDMatch.
Br1: Sample location: Kompolt-Kigyósér, Hungary
Gender: Female
Mt-DNA- K1c1
Approximate age: 1980-2190 cal BC
Description: The Great Hungarian Plain was a crossroads of cultural transformations that have shaped European prehistory. The authors had analysed a 5,000-year transect of human genomes, sampled from petrous bones giving consistently excellent endogenous DNA yields, from 13 Hungarian Neolithic, Copper, Bronze and Iron Age burials including two to high (~22 × ) and seven to ~1 × coverage, to investigate the impact of these on Europe’s genetic landscape. I converted the raw data of BR1 from Kompolt-Kigyósér site in Hungary into formats familiar to genetic genealogists. I also filtered with SNPs tested by DNA testing companies like FTDNA, 23andMe and Ancestry in order to upload to GEDMatch but found this ancient DNA has less SNPs that are common with them. Hence, I did not upload this to GEDMatch.
Br2: Sample location: Ludas-Varjú-dűlő, Hungary
Gedmatch kit number: F999933
Gender: Male
Y-DNA: J-M67
Mt-DNA: K1a1a
Approximate age: 1110-1270 cal BC
Description: The Great Hungarian Plain was a crossroads of cultural transformations that have shaped European prehistory. The authors had analysed a 5,000-year transect of human genomes, sampled from petrous bones giving consistently excellent endogenous DNA yields, from 13 Hungarian Neolithic, Copper, Bronze and Iron Age burials including two to high (~22 × ) and seven to ~1 × coverage, to investigate the impact of these on Europe’s genetic landscape. I converted the raw data of BR2 from Ludas-Varjú-dűlő site in Hungary into formats familiar to genetic genealogists. I also filtered with SNPs tested by DNA testing companies like FTDNA, 23andMe and Ancestry and upload to GEDMatch as kit# F999933.
Clovis Anzick-1: Sample location: Montana, North America
Gedmatch kit number: F999919
Gender: Male
Y-DNA: Q-Z780
Mt-DNA: D4h3a
Approximate Age: 12,500 years
Description: Clovis, with its distinctive biface, blade and osseous technologies, is the oldest widespread archaeological complex defined in North America. The genome sequence of a male infant (Anzick-1) recovered from the Anzick burial site in western Montana is available for download. I took this data and converted into familiar formats to genetic genealogists and also uploaded to GEdMatch.
CO1: Sample location: Apc-Berekalja I., Hungary
Gedmatch kit number: F999930
Gender: Female
Mt-DNA: H
Approximate Age: 2700-2900 cal BC
Description: The Great Hungarian Plain was a crossroads of cultural transformations that have shaped European prehistory. The authors had analysed a 5,000-year transect of human genomes, sampled from petrous bones giving consistently excellent endogenous DNA yields, from 13 Hungarian Neolithic, Copper, Bronze and Iron Age burials including two to high (~22 × ) and seven to ~1 × coverage, to investigate the impact of these on Europe’s genetic landscape. I converted the raw data of CO1 from Apc-Berekalja I. site in Hungary into formats familiar to genetic genealogists. I also filtered with SNPs tested by DNA testing companies like FTDNA, 23andMe and Ancestry and upload to GEDMatch as kit# F999930.
Denisova: Sample Location: Denisova Cave, Siberia
Gedmatch number: F999903
Gender: Female
Approximate age: 30,000 years
Description: The genome sequence of a Denisovan individual was generated from a small fragment of a finger bone discovered in Denisova Cave in southern Siberia in 2008. Approximately 30-fold coverage of the genome was generated using the Illumina GAIIx sequencing platform.
This project aims to convert the massive amount of data of Denisovan Genome to a raw data download file if FTDNA (or) 23andMe did the test. So, basically, I am just extracting the SNPs from Denisovan Genome and constructing the autosomal raw data file. This project is aimed to be more like factoids provided by FTDNA, just doing it from a hobbyist research perspective (and may produce scientific results). So, if you have a long strand/segment match which suggests that you are a cousin to Denisovan, don't blame me. The source files are taken from Denisovan DNA in VCF format. I used 2 laptops running 24/7 for nearly 2 weeks to parse ~ 1 terrabyte of Denisovan genome to produce the below results.
Gökhem2: Sample location: Sweden
Gedmatch number: F999934
Gender: Female
Mt-DNA: H1c
Approximate age: 5000 years
Description: The authors had generated between 0.01 to 2.2-fold genome wide coverage for 6 neolithic hunter-gathers from pitted ware culture, 4 neolithic farmers from funnel beaker culture and 1 late Mesolithic hunter-gatherer. I converted the raw data of Gökhem2 excavated in Sweden into formats familiar to genetic genealogists. I also filtered with SNPs tested by DNA testing companies like FTDNA, 23andMe and Ancestry and upload to GEDMatch as kit# F999934.
Hinxton-1: Sample location: Cambridgshire, UK
Gender: Male
Y-DNA: R-L151
Mt-DNA: K1a1b1b
Approximate age: 2000 years
Description: The authors had sequenced whole genome of 5 ancient DNA samples from skeletons excavated from Hinxton, Cambridgeshire, UK with estimated dates from the iron age through the Roman period (2500-1800 years ago). I converted these raw data of samples into formats familiar to genetic genealogists. I also filtered with SNPs tested by DNA testing companies like FTDNA, 23andMe and Ancestry in order to upload to GEDMatch but found some ancient DNA has less SNPs that are common with them. Hence, I did not upload those but the rest, I did upload to GEDMatch. Please note that the complete download is merged from several sequence runs and may not be sorted by coordinates.
Hinxton-2: Sample location: Cambridgshire, UK
Gedmatch kit number: F999921
Gender: Female
Mt-DNA: H2a2b1
Approximate age: 1300 years
Description: The authors had sequenced whole genome of 5 ancient DNA samples from skeletons excavated from Hinxton, Cambridgeshire, UK with estimated dates from the iron age through the Roman period (2500-1800 years ago). I converted these raw data of samples into formats familiar to genetic genealogists. I also filtered with SNPs tested by DNA testing companies like FTDNA, 23andMe and Ancestry in order to upload to GEDMatch but found some ancient DNA has less SNPs that are common with them. Hence, I did not upload those but the rest, I did upload to GEDMatch. Please note that the complete download is merged from several sequence runs and may not be sorted by coordinates.
Hinxton-3: Sample location: Cambridgshire, UK
Gedmatch kit number: F999922
Gender: Female
MT-DNA: K1a4a1a2b
Approximate age: 1300 years
Description: The authors had sequenced whole genome of 5 ancient DNA samples from skeletons excavated from Hinxton, Cambridgeshire, UK with estimated dates from the iron age through the Roman period (2500-1800 years ago). I converted these raw data of samples into formats familiar to genetic genealogists. I also filtered with SNPs tested by DNA testing companies like FTDNA, 23andMe and Ancestry in order to upload to GEDMatch but found some ancient DNA has less SNPs that are common with them. Hence, I did not upload those but the rest, I did upload to GEDMatch. Please note that the complete download is merged from several sequence runs and may not be sorted by coordinates.
Hinxton-4: Sample location: Cambridgshire, UK
Gedmatch kit number: F999925
Gender: Male
Y-DNA: R-DF25
Mt-DNA: H1ag1
Approximate age: 2000 years
Description: The authors had sequenced whole genome of 5 ancient DNA samples from skeletons excavated from Hinxton, Cambridgeshire, UK with estimated dates from the iron age through the Roman period (2500-1800 years ago). I converted these raw data of samples into formats familiar to genetic genealogists. I also filtered with SNPs tested by DNA testing companies like FTDNA, 23andMe and Ancestry in order to upload to GEDMatch but found some ancient DNA has less SNPs that are common with them. Hence, I did not upload those but the rest, I did upload to GEDMatch. Please note that the complete download is merged from several sequence runs and may not be sorted by coordinates.
Hinxton-5: Sample location: Cambridgshire, UK
Gedmatch kit number: F999926
Gender: Female
Mt-DNA: H2a2a1
Approximate age: 1300 years
Description: The authors had sequenced whole genome of 5 ancient DNA samples from skeletons excavated from Hinxton, Cambridgeshire, UK with estimated dates from the iron age through the Roman period (2500-1800 years ago). I converted these raw data of samples into formats familiar to genetic genealogists. I also filtered with SNPs tested by DNA testing companies like FTDNA, 23andMe and Ancestry in order to upload to GEDMatch but found some ancient DNA has less SNPs that are common with them. Hence, I did not upload those but the rest, I did upload to GEDMatch. Please note that the complete download is merged from several sequence runs and may not be sorted by coordinates.
IR1: Sample location: Ludas-Varjú-dűlő, Hungary
Gedmatch kit number: F999929
Gender: Male
Y-DNA: N-M231
Mt-DNA: G2a1
Approximate age: 830-980 cal BC
Description: The Great Hungarian Plain was a crossroads of cultural transformations that have shaped European prehistory. The authors had analysed a 5,000-year transect of human genomes, sampled from petrous bones giving consistently excellent endogenous DNA yields, from 13 Hungarian Neolithic, Copper, Bronze and Iron Age burials including two to high (~22 × ) and seven to ~1 × coverage, to investigate the impact of these on Europe’s genetic landscape. I converted the raw data of IR1 from Ludas-Varjú-dűlő site in Hungary into formats familiar to genetic genealogists. I also filtered with SNPs tested by DNA testing companies like FTDNA, 23andMe and Ancestry and upload to GEDMatch as kit# F999929.
KO1: Sample location: Tiszaszőlős-Domaháza, Hungary
Gedmatch kit number: F999931
Gender: male
Y-DNA: I-L68
Mt-DNA: R3
Approximate age: 5650-5780 cal BC
Description: The Great Hungarian Plain was a crossroads of cultural transformations that have shaped European prehistory. The authors had analysed a 5,000-year transect of human genomes, sampled from petrous bones giving consistently excellent endogenous DNA yields, from 13 Hungarian Neolithic, Copper, Bronze and Iron Age burials including two to high (~22 × ) and seven to ~1 × coverage, to investigate the impact of these on Europe’s genetic landscape. I converted the raw data of KO1 from Tiszaszőlős-Domaháza site in Hungary into formats familiar to genetic genealogists. I also filtered with SNPs tested by DNA testing companies like FTDNA, 23andMe and Ancestry and upload to GEDMatch as kit# F999931.
Kostenki14: Sample location: European Russia
Gedmatch kit number: F999936
Gender: Male
Y-DNA: C-V199
MT-DNA: U2
Approximate age: 38,700-36,200 years
Description: The origin of contemporary Europeans remains contentious. The authors obtained a genome sequence from Kostenki 14 in European Russia dating to 38,700 to 36,200 years ago, one of the oldest fossils of Anatomically Modern Humans from Europe. I converted this raw data of Kostenki 14 into formats familiar to genetic genealogists. I also filtered with SNPs tested by DNA testing companies like FTDNA, 23andMe and Ancestry and upload to GEDMatch as kit# F999936.
La Brańa-Arintero: Sample location: León, Spain
Gedmatch kit number: F999915
Gender: Male
Y-DNA: C-V183
mt-DNA: U5b2c1
Approximate age: 7,000 years
Description: Approximately 7,000-year-old Mesolithic skeleton discovered at the La Brańa-Arintero site in León, Spain, had been sequenced to retrieve a complete pre-agricultural European human genome and the sequence reads were made available to public by the authors. I converted these raw sequence reads supplied in the scientific paper to formats familiar with genetic genealogists.
Linearbandkeramik (LBK): Sample location: Stuttgart, Germany
Gedmatch kit number: F999916
Gender: Female
Mt-DNA: T2c2
Approximate Age: 7,500 years
Description: To investigate European population history around the time of the agricultural transition, the authors sequenced complete genomes from a ~7,500 year old early farmer from the Linearbandkeramik (LBK) culture from Stuttgart in Germany. I converted this raw data into formats familiar to genetic genealogists.
Loschbour: Sample location: Loschbour, Luxembourg
Gedmatch kit number: F999918
Gender: Male
Y-DNA: I-L460
Mt-DNA: U5b1a
Approximate age: 8,000 years
Description: To investigate European population history around the time of the agricultural transition, the authors sequenced complete genomes from a ~8,000 year old skeleton from the Loschbour rock shelter in Heffingen, Luxembourg. I converted this raw data into formats familiar to genetic genealogists.
Mal'ta: Sample location: South - Central Siberia
Gedmatch kit number: F999914
Gender: Male
Y-DNA: R
Mt-DNA:U
Approximate age: 24,000 years
Description: The origins of the First Americans remain contentious. Although Native Americans seem to be genetically most closely related to east Asians there is no consensus with regard to which specific Old World populations they are closest to. Here the authors sequence an ancient genome of individual (MA-1), from Mal’ta in south-central Siberia, to an average depth of 1x. Based on the author knowledge, this MA-1 DNA is the oldest anatomically modern human genome reported to date. I converted this raw sequence reads supplied in this scientific paper to formats familiar with genetic genealogists.
Motala12: Sample location: Östergötland, Sweden
Gedmatch kit number: F999917
Gender: male
Y-DNA: I-L460
Mt-DNA: U2e1
Approximate age: 7,000 years
Description: The Motala samples come from the site of Kanaljorden in the town of Motala, Östergötland, Sweden. The site was excavated between 2009 and 2013. The authors state that these samples are between 7,013 and 6,701 years old. I converted the raw data supplied in this scientific paper to formats familiar with genetic genealogists. I also filtered with SNPs tested by DNA testing companies like FTDNA, 23andMe and Ancestry in order to upload to GEDMatch but found this ancient DNA has less SNPs that are common with them except Motala-12. Hence, I am not uploading the rest to GEDMatch. Motala-1, Motala-2, Motala-3, Motala-4, Motala-6, Motala-9 and Motala-12 are available for download.
NE1: Sample location: Polgár-Ferenci-hát, Hungary
Gedmatch kit number: F999937
Gender: Female
Mt-DNA: U5b2c
Approximate age: 5070-5310 cal BC
Description: The Great Hungarian Plain was a crossroads of cultural transformations that have shaped European prehistory. The authors had analysed a 5,000-year transect of human genomes, sampled from petrous bones giving consistently excellent endogenous DNA yields, from 13 Hungarian Neolithic, Copper, Bronze and Iron Age burials including two to high (~22 × ) and seven to ~1 × coverage, to investigate the impact of these on Europe’s genetic landscape. I converted the raw data of NE1 from Polgár-Ferenci-hát site in Hungary into formats familiar to genetic genealogists. I also filtered with SNPs tested by DNA testing companies like FTDNA, 23andMe and Ancestry and uploaded to GEDmatch as kit# F999937.
NE5: Sample location: Kompolt - Kigyósér, Hungary
Gedmatch kit number: F999927
Gender: Male
Y-DNA: C-F3393
MT-DNA: J1c
Approximate age: 4990-5210 cal BC
Description: The Great Hungarian Plain was a crossroads of cultural transformations that have shaped European prehistory. The authors had analysed a 5,000-year transect of human genomes, sampled from petrous bones giving consistently excellent endogenous DNA yields, from 13 Hungarian Neolithic, Copper, Bronze and Iron Age burials including two to high (~22 × ) and seven to ~1 × coverage, to investigate the impact of these on Europe’s genetic landscape. I converted the raw data of NE5 from Kompolt-Kigyósér site in Hungary into formats familiar to genetic genealogists. I also filtered with SNPs tested by DNA testing companies like FTDNA, 23andMe and Ancestry and upload to GEDMatch as kit# F999927.
NE6: Sample location: Apc-Berekalja I., Hungary
Gedmatch kit number: F999932
Gender: Male
Y-DNA: C-P255
Mt-DNA: K1a3a3
Approximate age: 4950-5300 cal BC
Description: The Great Hungarian Plain was a crossroads of cultural transformations that have shaped European prehistory. The authors had analysed a 5,000-year transect of human genomes, sampled from petrous bones giving consistently excellent endogenous DNA yields, from 13 Hungarian Neolithic, Copper, Bronze and Iron Age burials including two to high (~22 × ) and seven to ~1 × coverage, to investigate the impact of these on Europe’s genetic landscape. I converted the raw data of NE6 from Apc-Berekalja I. site in Hungary into formats familiar to genetic genealogists. I also filtered with SNPs tested by DNA testing companies like FTDNA, 23andMe and Ancestry and upload to GEDMatch as kit# F999932.
NE7: Sample location: Apc-Berekalja I., Hungary
Gedmatch kit number: F999928
Gender: Male
Y-DNA: I-L1228
MT-DNA: N1a
Approximate age: 4360-4490 cal BC
Description: The Great Hungarian Plain was a crossroads of cultural transformations that have shaped European prehistory. The authors had analysed a 5,000-year transect of human genomes, sampled from petrous bones giving consistently excellent endogenous DNA yields, from 13 Hungarian Neolithic, Copper, Bronze and Iron Age burials including two to high (~22 × ) and seven to ~1 × coverage, to investigate the impact of these on Europe’s genetic landscape. I converted the raw data of NE7 from Apc-Berekalja I. site in Hungary into formats familiar to genetic genealogists. I also filtered with SNPs tested by DNA testing companies like FTDNA, 23andMe and Ancestry and upload to GEDMatch as kit# F999928.
Palaeo Eskimo: Sample location: Qeqertarsuaq, Greenland
Gedmatch kit number: F999906
Gender: male
Y-DNA: Q1a
Mt-DNA: D2a1
Approximate age: 4,000 years
Description: The Saqqaq Genome Project generated 20x sequence coverage over the genome of an individual from the Extinct Palaeo-Eskimo Saqqaq culture. The project was a large collaboration between many Centres across the world, coordinated by Professor Eske Willerslev from the Centre for GeoGenetics at University of Copenhagen, Denmark. Full details of authors and the cooperation can be obtained from the Feb 2010 article referenced below.
This project aims to convert the raw data of the extinct Palaeo-Eskimo Genome to a raw data download file if FTDNA (or) 23andMe did the test. So, basically, I am just extracting the SNPs from the Genome and constructing the autosomal raw data file. This project is aimed to be more like factoids provided by FTDNA, just doing it from a hobbyist research perspective (and may produce scientific results). The source files are taken from Data for the Saqqaq genome project.
Ust'-Ishim: Sample location: Ust'-Ishim, Siberia
Gedmatch kit number: F999935
Gender: Male
Y-DNA: K-M526
Mt-DNA: R
Approximate age: 45,000 years
Description: The authors provided a high-quality genome sequence of a 45,000-year-old modern human from Siberia. I converted this raw data of Ust'-Ishim into formats familiar to genetic genealogists. I also filtered with SNPs tested by DNA testing companies like FTDNA, 23andMe and Ancestry and upload to GEDMatch as kit# F999935.
Vi33. 16 Neanderthal: Sample location: Vindija cave, Croatia
Gender: Female
Approximate age: Vindija cave, Croatia
Description: Authors had provided Neanderthal genomes with their publications. I converted the raw data of Vi33.16 sample into formats familiar to genetic genealogists. I also filtered with SNPs tested by DNA testing companies like FTDNA, 23andMe and Ancestry in order to upload to GEDMatch but found this ancient DNA has less SNPs that are common with them. Hence, I did not upload this to GEDMatch. However, complete SNPs and filtered SNPs are available for download.
Vi33. 25 Neanderthal: Sample location: Vindija cave, Croatia
Gender: female
Approximate age: N/A
Description: Authors had provided Neanderthal genomes with their publications. I converted the raw data of Vi33.25 sample into formats familiar to genetic genealogists. I also filtered with SNPs tested by DNA testing companies like FTDNA, 23andMe and Ancestry in order to upload to GEDMatch but found this ancient DNA has less SNPs that are common with them. Hence, I did not upload this to GEDMatch. However, complete SNPs are available for download.
Vi33. 26 Neanderthal: Sample location: Vindija cave, Croatia
Gender: Female
Approximate age: 44,450 years
Description: Authors had provided Neanderthal genomes with their publications. I converted the raw data of Vi33.25 sample into formats familiar to genetic genealogists. I also filtered with SNPs tested by DNA testing companies like FTDNA, 23andMe and Ancestry in order to upload to GEDMatch but found this ancient DNA has less SNPs that are common with them. Hence, I did not upload this to GEDMatch. However, complete SNPs are available for download.
Ex. My results:
Ajvide 58: 3.24%
Altai Neanderthal: 1.95%
Australian Aboriginal: 5.80%
Br1: 6.73%
Br2: 33.77%
Clovis Anzick-1: 22.99%
CO1: 8.02%
Denisova: 1.35%
Gökhem2: 4.52%
Hinxton-1: 2.04%
Hinxton-2: 2.30%
Hinxton-3: 2.91%
Hinxton-4: 4.97%
Hinxton-5: 2.34%
IR1: 8.54%
KO1: 10.14%
Kostenki14: 12.24%
La Brańa-Arintero: 10.37%
Linearbandkeramik (LBK): 31.43%
Loschbour: 27.51%
Mal'ta: 6.58%
Motala12: 12.37%
NE1: 31.59%
NE5: 7.79%
NE6: 8.33%
NE7: 8.02%
Palaeo Eskimo: 9.25%
Ust'-Ishim: 27.37%
Vi33. 16 Neanderthal: .52%
Vi33. 25 neanderthal: 1%
Vi33. 26 Neanderthal: .87%
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Originally Posted by Armstrong
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